[QE-users] Underestimated Adsorption Energy with optB88-vdW
Gabriel Bramley
G.A.Bramley at soton.ac.uk
Fri Oct 16 14:50:53 CEST 2020
Dear Tamas,
I sincerely hope they're using the same basis!
So I've ran a further test with the later DFX type vdW corrections and I notice that these functional yield (expected) overestimated adsorption energies, but within a sensible tolerance. I also notice there are QC tests for DF2 and DF3 type vdW corrections, but no benchmarking for DF1. Given we've eliminated the system, dipole correction, exchange functional and the other vdW type functionals give sensible values, I'm tempted to say there's an issue with the DF1 type correction specifically. I will contact the developers with this issue.
You have been a massive help. Thank you very much for your helpful suggestions.
Kind regards,
Gabriel Bramley
________________________________
From: users <users-bounces at lists.quantum-espresso.org> on behalf of Tamas Karpati <tkarpati at gmail.com>
Sent: 16 October 2020 13:03
To: Quantum ESPRESSO users Forum <users at lists.quantum-espresso.org>
Subject: Re: [QE-users] Underestimated Adsorption Energy with optB88-vdW
Dear Gabriel,
Good news. I assume ecutwfc (+ecutrho) and k point
density are also the same (thus having the same amount of
systematic offset). I guess the deviation is from another
source. One more thing I can think of is the basis being used.
Is it possible for you to use the exact same PW basis in
each software? I hope so. If not, I have no idea -except for an
implementation difference...
I rechecked the corresponding source and found (also referred
to by INPUT_PW.html @ input_dft) it to be Modules/funct.f90.
I do not know how it relates to the LIBXC+QE combo, guess
it's just the QE internal machinery -with a useful list of
functionals and numbering in the lengthy comments.
I hope it helps but I cannot contribute more to this.
Good luck,
t
On Thu, Oct 15, 2020 at 12:32 AM Gabriel Bramley
<G.A.Bramley at soton.ac.uk> wrote:
>
> Dear Thomas,
>
> Apologies for the lack of clarity. Yes, they are.
> I have checked this and they appear correct. I believe the numbers represent (exchange, correlation, gradient corrected exchange, gradient corrected correlation, meta GGA and vdW (non-local correlation) correction). obk8 is specified as (slater, Perdew Wang, optB88x, p86c, no meta GGA, no vdW correction) and vdwdf-obk8 is specified as (slater, Perdew Wang, optB88x, no gradient corrected correlation, no meta GGA, DF-vdW1), which looks correct to me, as the E_xc term in the original optB88-vdW paper consists of E_xc = E^GGA_x + E^LDA_c + E^nl(vdW)_c. However, there might be some nuance I am missing. Further, I've had a look in the code itself (xc_df_vdW) and how it relates to the core PW-SCF and nothing jumps out as being out of the ordinary, but I'm not familiar enough with the QE code to make a complete judgement on that.
>
> I've run further calculations with the LIBXC library (using their version of optb88 exchange), and that doesn't yield improvement either.
>
> Kind regards,
> Gabriel Bramley
> ________________________________
> From: users <users-bounces at lists.quantum-espresso.org> on behalf of Tamas Karpati <tkarpati at gmail.com>
> Sent: 12 October 2020 12:53
> To: Quantum ESPRESSO users Forum <users at lists.quantum-espresso.org>
> Subject: Re: [QE-users] Underestimated Adsorption Energy with optB88-vdW
>
> Dear Gabriel,
> 1, The same box size everywhere, or not?
> 2, QE reports near the beginning of its output a series of 6 or 7 numbers,
> each indicating a term in the functional. Cannot now recall which
> but -if you cannot find- I can check in a week the source file that
> actually lists them (just easy comments, no code).
> Also, if a dispersion term is applied pw.x reports it somewhat below
> (in connection with the vdw_corr input parameter).
> I hope it helps to identify what theory you are actually using.
> (Note: input_dft overwrites the functional specification of the UPF file
> but vdW terms are just additive, not exclusive -if i'm correct).
> HTH.
> t
>
>
> On Fri, Oct 9, 2020 at 3:28 PM Gabriel Bramley <G.A.Bramley at soton.ac.uk> wrote:
> >
> > Hello Thomas,
> >
> > Yes, the box size should be converged for the dipole corrections specified (over twice the length in the z-direction of the initial system itself). I've just ran a few tests using an incredibly large box size (50 Ang) and the enthalpy value remains similarly low compared to literature values.
> >
> > I'm thinking your second suggestion is quite likely. The calculation does output a non-local correlation energy in the high verbosity mode, but perhaps the relevant terms aren't being added correctly in the final total energy. I will report back once I've looked into this more thoroughly.
> >
> > Thank you for your input
> >
> > Kind regards,
> > Gabriel
> > ________________________________
> > From: users <users-bounces at lists.quantum-espresso.org> on behalf of Tamas Karpati <tkarpati at gmail.com>
> > Sent: 08 October 2020 07:51
> > To: Quantum ESPRESSO users Forum <users at lists.quantum-espresso.org>
> > Subject: Re: [QE-users] Underestimated Adsorption Energy with optB88-vdW
> >
> > Dear Gabriel,
> > By "consistent box" sizes do you mean that you have
> > converged the box sizes for all three species?
> > I rather meant the exact same box size for all
> > (and this size be converged, ie. large enough for each).
> >
> > BTW, the systematic differences you observed might be
> > due to a vdW (or another) term switched on/off
> > (or a bug/error in code/functional).
> > Make sure, everything is treated appropriately.
> > For instance, input_dft can be trickier than you expect 1st.
> > Doubly disperse the functional (in both input_dft and
> > vdw_corr) might do sg. similar.
> > Bests,
> > t
> >
> > On Wed, Oct 7, 2020 at 2:17 PM Gabriel Bramley <G.A.Bramley at soton.ac.uk> wrote:
> > >
> > > Hello Thomas,
> > >
> > > 1/2
> > >
> > > They haven't specified any parameters to my knowledge that would lead to such a large error. There may be slight difference in the thresholds of energetic convergence, but they should yield errors on a much smaller scale.
> > >
> > > 2/2
> > >
> > > RE: box sizes - We did briefly fall foul of having inconsistent box sizes for one or two calculations, but this is definitely a problem we've addressed. (We use slightly different box sizes for the adsorbate, but I've ran a few different cell sizes for this small molecules and it yielded very small differences).
> > >
> > > And you're quite right, I do apologise, that should be written as:
> > > E_adsorption = E_(slab+adsorbate) - (E_slab + E_adsorbate)
> > >
> > > Kind regards,
> > > Gabriel
> > >
> > >
> > > ________________________________
> > > From: users <users-bounces at lists.quantum-espresso.org> on behalf of Tamas Karpati <tkarpati at gmail.com>
> > > Sent: 07 October 2020 11:57
> > > To: Quantum ESPRESSO users Forum <users at lists.quantum-espresso.org>
> > > Subject: Re: [QE-users] Underestimated Adsorption Energy with optB88-vdW
> > >
> > > Dear Gabriel,
> > >
> > > 1/2, are your sims. reproducing *all* of the ref. params? (eg. are
> > > cell parameters the same?)
> > > any missing params. would contribute by adding an *unknown*
> > > magnitude of error...
> > > 2/2, my guess would be that your evaluation of dE_a is wrong due to
> > > *different cell sizes*
> > > (basis set superposition error?); this would explain the
> > > systematic character of the deviation
> > > and suggest (pain indeed) to increase cell sizes up to the same
> > > (ie. the largest) of
> > > E_slab+ads, E_slab and E_adsorbant.
> > > +1, your eq. for the heat is recursive (kidding): LHS is to be renamed!
> > >
> > > HTH,
> > > t
> > >
> > > On Wed, Oct 7, 2020 at 12:19 PM Gabriel Bramley <G.A.Bramley at soton.ac.uk> wrote:
> > > >
> > > > Dear Users,
> > > >
> > > > Problem:
> > > >
> > > > I am performing calculations with the optB88-vdW functional to obtain adsorption energies of small aromatic molecules on metallic surface facets (Pt(111) and phenol for the cases discussed here). Unfortunately, the adsorption energies obtained from these calculations are systematically 50 kJ mol^-1 below comparable studies performed with VASP. I have replicated their parameters as closely as possible - as such I am also using PBE PAW pseudopotentials from the psl pseudopotential library.
> > > >
> > > > The above underestimation occurs for a fully periodic calculation. Using the dipole corrections (2D and ESM (bc1)) appears to exacerbate these issues, leading to a 70 kJ mol^-1 underestimation of the adsorption energy. (The system is centred in the centre of the cell with 8 Ang of vacuum either side of the system for 2D, and the system is centred around z=0 for ESM).
> > > >
> > > > The calculation for adsorption energy is performed as:
> > > > E_ads = E_slab+ads - (E_slab + E_ads)
> > > > Where the adsorbate is calculated in a 30x30x30 Ang cell with the Markov-Payne dipole correction (Though this give negligable difference compared to full PBC).
> > > >
> > > > Question:
> > > >
> > > > The PBE+rvv10 functional performs significantly better with PBC and 2D Coulomb Cutoff, giving sensible and expected values for the adsorption energy. However, I am cautious in trusting these results given the large errors for the optB88-vdW functional. Is there something obvious I am missing in these calculations or is this a known issue?
> > > >
> > > > A previous email to this list has pointed out other issues with this functional (https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.mail-archive.com%2Fusers%40lists.quantum-espresso.org%2Fmsg35965.html&data=04%7C01%7CG.A.Bramley%40soton.ac.uk%7Cc2f931b9b5174bb4aede08d871cb2f3f%7C4a5378f929f44d3ebe89669d03ada9d8%7C0%7C0%7C637384464788255700%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=D4Lv5C%2FNV8PfrvO2XKFwAHcBpzpmbqxv0c6RTQaW%2FOM%3D&reserved=0). This might help, but could someone please clarify this as well?
> > > >
> > > > Additional information:
> > > >
> > > > I am using QE v.6.5 compiled with Intel-2018 with the ELPA 2017 library. Enivron Module installed but not used in these calculations. All QC tests pass without error.
> > > >
> > > > Please find below the input file:
> > > >
> > > > ___________________________________
> > > >
> > > > &CONTROL
> > > > calculation = 'relax'
> > > > restart_mode = 'from_scratch'
> > > > prefix = 'Pt'
> > > > disk_io = 'low'
> > > > pseudo_dir = '/home/gab1u17/pslib-kj-paw/'
> > > > nstep = 300
> > > > /
> > > > &SYSTEM
> > > > ibrav = 0
> > > > ecutwfc = 45
> > > > ecutrho = 360
> > > > occupations = 'smearing'
> > > > degauss = 0.05
> > > > smearing = 'gaussian'
> > > > input_dft = 'vdw-df-obk8'
> > > > assume_isolated = '2D'
> > > > ntyp = 4
> > > > nat = 48
> > > > /
> > > > &ELECTRONS
> > > > electron_maxstep = 150
> > > > conv_thr = 8e-08
> > > > mixing_mode = 'local-TF'
> > > > mixing_beta = 0.2
> > > > /
> > > > &IONS
> > > > ion_dynamics = 'bfgs'
> > > > /
> > > > &CELL
> > > > /
> > > >
> > > > ATOMIC_SPECIES
> > > > Pt 195.084 Pt.pbe-n-kjpaw_psl.1.0.0.UPF
> > > > C 12.011 C.pbe-n-kjpaw_psl.1.0.0.UPF
> > > > O 15.999 O.pbe-n-kjpaw_psl.1.0.0.UPF
> > > > H 1.008 H.pbe-n-kjpaw_psl.1.0.0.UPF
> > > >
> > > > K_POINTS automatic
> > > > 6 6 1 0 0 0
> > > >
> > > > CELL_PARAMETERS angstrom
> > > > 7.42718991274627 0.00000000000000 0.00000000000000
> > > > 3.71359495637314 6.43213514316980 0.00000000000000
> > > > 0.00000000000000 0.00000000000000 29.000000000003126
> > > >
> > > > ATOMIC_POSITIONS angstrom
> > > > Pt 2.5641489000 0.4594382200 8.0000000000 0 0 0
> > > > Pt 5.2167167200 1.3783146700 8.0000000000 0 0 0
> > > > ...
> > > > Pt 4.1556895900 0.1531460700 17.1683222700
> > > > Pt 6.8082574200 1.0720225200 17.1683222700
> > > > Pt 2.0336353300 1.9908989700 17.1683222700
> > > > ...
> > > > H 0.3060672802 1.6388023741 19.1376040000
> > > > H 2.7167357186 1.0284278006 19.1376040000
> > > > H 4.4562891110 2.8078620154 19.1376040000
> > > >
> > > > ___________________________________
> > > >
> > > > Thank you in advance for your assistance.
> > > >
> > > > Kind regards,
> > > > Gabriel Bramley
> > > > PhD. Candidate
> > > > University of Southampton
> > > >
> > > > _______________________________________________
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